13 #include "Transcript.h"
14 #include "Transcripts.h"
22 ChrInfo(const string& name, size_t len) {
27 bool operator< (const ChrInfo& o) const {
34 vector<GTFItem> items;
36 vector<int> starts; // used to generate .grp
37 map<string, vector<int> > sn2tr; // map from seqname to transcripts
38 map<string, vector<int> >::iterator iter;
39 vector<ChrInfo> chrvec;
41 Transcripts transcripts;
43 char groupF[STRLEN], tiF[STRLEN], refFastaF[STRLEN];
44 char chromListF[STRLEN];
47 char mappingFile[STRLEN];
49 map<string, string> mi_table; // mapping info table
50 map<string, string>::iterator mi_iter; //mapping info table's iterator
52 void loadMappingInfo(char* mappingF) {
53 ifstream fin(mappingF);
54 string line, key, value;
57 fprintf(stderr, "Cannot open %s! It may not exist.\n", mappingF);
62 while (getline(fin, line)) {
63 line = cleanStr(line);
64 if (line[0] == '#') continue;
65 istringstream strin(line);
67 mi_table[key] = value;
73 bool buildTranscript(int sp, int ep) {
74 int cur_s, cur_e; // current_start, current_end
77 string transcript_id = items[sp].getTranscriptID();
78 string gene_id = items[sp].getGeneID();
79 char strand = items[sp].getStrand();
80 string seqname = items[sp].getSeqName();
81 string left = items[sp].getLeft();
85 for (int i = sp; i <= ep; i++) {
86 int start = items[i].getStart();
87 int end = items[i].getEnd();
89 assert(strand == items[i].getStrand());
90 assert(seqname == items[i].getSeqName());
92 if (cur_e + 1 < start) {
93 if (cur_s > 0) vec.push_back(Interval(cur_s, cur_e));
96 cur_e = (cur_e < end ? end : cur_e);
98 if (cur_s > 0) vec.push_back(Interval(cur_s, cur_e));
100 transcripts.add(Transcript(transcript_id, gene_id, seqname, strand, vec, left));
105 void parse_gtf_file(char* gtfF) {
107 string line, curgid, tid, gid; // curgid: current gene id;
110 if (!fin.is_open()) { fprintf(stderr, "Cannot open %s! It may not exist.\n", gtfF); exit(-1); }
115 while (getline(fin, line)) {
116 if (line[0] == '#') continue; // if this line is comment, jump it
118 string feature = item.getFeature();
119 if (feature == "exon") {
120 if (item.getStart() > item.getEnd()) {
121 fprintf(stderr, "Warning: exon's start position is larger than its end position! This exon is discarded.\n");
122 fprintf(stderr, "\t%s\n\n", line.c_str());
124 else if (item.getStart() < 1) {
125 fprintf(stderr, "Warning: exon's start position is less than 1! This exon is discarded.\n");
126 fprintf(stderr, "\t%s\n\n", line.c_str());
129 if (hasMappingFile) {
130 tid = item.getTranscriptID();
131 mi_iter = mi_table.find(tid);
132 if (mi_iter == mi_table.end()) {
133 fprintf(stderr, "Mapping Info is not correct, cannot find %s's gene_id!\n", tid.c_str());
136 //assert(iter != table.end());
137 gid = mi_iter->second;
140 items.push_back(item);
145 if (verbose && cnt % 200000 == 0) { printf("Parsed %d lines\n", cnt); }
149 sort(items.begin(), items.end());
155 int sp = 0, ep; // start pointer, end pointer
156 int nItems = items.size();
158 while (sp < nItems) {
159 tid = items[sp].getTranscriptID();
160 gid = items[sp].getGeneID();
163 while (ep < nItems && items[ep].getTranscriptID() == tid) ep++;
166 buildTranscript(sp, ep);
168 int sid = transcripts.getM();
169 const Transcript& transcript = transcripts.getTranscriptAt(sid);
172 starts.push_back(sid);
175 iter = sn2tr.find(transcript.getSeqName());
176 if (iter == sn2tr.end()) {
177 vector<int> vec(1, sid);
178 sn2tr[transcript.getSeqName()] = vec;
181 iter->second.push_back(sid);
187 M = transcripts.getM();
188 starts.push_back(M + 1);
192 fprintf(stderr, "Number of transcripts in the reference is less than 1!\n");
196 if (verbose) { printf("Parsing gtf File is done!\n"); }
200 if (!isalpha(c)) { fprintf(stderr, "Sequence contains unknown letter '%c'!\n", c); exit(-1); }
201 //assert(isalpha(c));
202 if (isupper(c) && c != 'A' && c != 'C' && c != 'G' && c != 'T') c = 'N';
203 if (islower(c) && c != 'a' && c != 'c' && c != 'g' && c != 't') c = 'n';
207 void writeResults(char* refName) {
211 sprintf(groupF, "%s.grp", refName);
212 sprintf(tiF, "%s.ti", refName);
213 sprintf(refFastaF, "%s.transcripts.fa", refName);
214 sprintf(chromListF, "%s.chrlist", refName);
219 for (int i = 0; i < s; i++) fout<<starts[i]<<endl;
221 if (verbose) { printf("Group File is generated!\n"); }
223 transcripts.writeTo(tiF);
224 if (verbose) { printf("Transcript Information File is generated!\n"); }
226 fout.open(chromListF);
228 for (int i = 0; i < s; i++) {
229 fout<<chrvec[i].name<<'\t'<<chrvec[i].len<<endl;
232 if (verbose) { printf("Chromosome List File is generated!\n"); }
234 fout.open(refFastaF);
235 for (int i = 1; i <= M; i++) {
236 fout<<">"<<transcripts.getTranscriptAt(i).getTranscriptID()<<endl;
240 if (verbose) { printf("Extracted Sequences File is generated!\n"); }
243 int main(int argc, char* argv[]) {
244 if (argc < 6 || (hasMappingFile = atoi(argv[4])) && argc < 7) {
245 printf("Usage: rsem-extract-reference-transcripts refName quiet gtfF hasMappingFile [mappingFile] chromosome_file_1 [chromosome_file_2 ...]\n");
249 verbose = !atoi(argv[2]);
250 if (hasMappingFile) {
251 loadMappingInfo(argv[5]);
253 parse_gtf_file(argv[3]);
256 string line, gseq, seqname;
262 seqs.resize(M + 1, "");
263 int start = hasMappingFile ? 6 : 5;
264 for (int i = start; i < argc; i++) {
266 if (!fin.is_open()) { fprintf(stderr, "Cannot open %s! It may not exist.\n", argv[i]); exit(-1); }
267 pt = getline(fin, line);
268 while (pt != 0 && line[0] == '>') {
269 istringstream strin(line.substr(1));
273 while((pt = getline(fin, line)) && line[0] != '>') {
277 size_t len = gseq.length();
279 for (size_t j = 0; j < len; j++) gseq[j] = check(gseq[j]);
281 iter = sn2tr.find(seqname);
282 if (iter == sn2tr.end()) continue;
284 chrvec.push_back(ChrInfo(seqname, len));
286 vector<int>& vec = iter->second;
288 for (int j = 0; j < s; j++) {
289 assert(vec[j] > 0 && vec[j] <= M);
290 transcripts.getTranscriptAt(vec[j]).extractSeq(gseq, seqs[vec[j]]);
295 if (verbose) { printf("%s is processed!\n", argv[i]); }
298 for (int i = 1; i <= M; i++) {
300 fprintf(stderr, "%s's sequence is empty! You must provide all chromosome files of transcripts which are presented in the .gtf file!\n", transcripts.getTranscriptAt(i).getTranscriptID().c_str());
305 sort(chrvec.begin(), chrvec.end());
307 if (verbose) { printf("Extracting sequences is done!\n"); }
309 writeResults(argv[1]);